› 2dfd

X-ray diffraction
1.9Å resolution

Crystal Structure of Human Malate Dehydrogenase Type 2

Released:
DOI: 10.2210/pdb2dfd/pdb
PDB entry 2dfd coloured by chain, front view.
PDB entry 2dfd coloured by chain, side view.
PDB entry 2dfd coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Ugochukwu E, Shafqat N, Rojkova A, Sundstrom M, Arrowsmith C, Weigelt J, Edwards A, von Delft F, Oppermann U, Structural Genomics Consortium (SGC)

Function and Biology Details

Reaction catalysed: 
(S)-malate + NAD(+) = oxaloacetate + NADH
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assemblies composition:
homo dimer (preferred)
homo tetramer
Assembly name:
PDBe Complex ID:
PDB-CPX-154207 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Malate dehydrogenase, mitochondrial Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 342 amino acids
Theoretical weight: 36.24 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P40926 (Residues: 19-338; Coverage: 95%)
Gene name: MDH2
Sequence domains:
Structure domains:

Ligands and Environments


Cofactor: Ligand NAD 4 x NAD
4 bound ligands:
Ligand MLT 4 x MLT
Ligand CL 7 x CL
Ligand HIS 3 x HIS
Ligand ALA 1 x ALA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 59.943Å b: 152.526Å c: 154.827Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.158 0.156 0.194
Expression system: Escherichia coli

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